#!/bin/zsh -f
# 
version="0.5"

##  sca2mtz.zsh

print "#####################################################################################################"
print ""
print "  This script will process the sca file output from SCALEPACK using CCP4 programs"
print "  including truncate, uniquify, and (optionally) mtz2various to"
print "  produce reduced data in CCP4 format and (optionally) CNS format.  The script employs"
print "  OS X interface dialogs and is meant to be run interactively.  Use this by issuing"
print "  sca2mtz.zsh and optionally the sca file to be processed.  It requires CCP4 to be installed"
print "  (preferably via fink) and the Camino web browser (the Cocoa version of Mozilla/Netscape)."
print ""
print "#####################################################################################################"
print ""
# 
#   

# This starts X-windows if it hasn't started already.
open -a X11

# Make sure CCP4 is initialized  (reality check)

if [[ -z $CCP4_BIN ]]; then
	if [[ -f /sw/bin/init.sh ]]; then
      . /sw/bin/init.sh
	fi
fi

if [[ -z $CCP4_BIN ]]; then
	print "I can't find CCP4."
	print "Terminating program.  Make sure ccp4 is initialized."
	return 1
fi

# Now define some functions to get needed input parameters from the user

################################################################################
# function GetProjectName lets user specify the CCP4 Project Name (optional)

function GetProjectName {
    osascript << eof-1
        tell app "Finder"
            activate
            set prompt to "Enter a CCP4 PROJECTNAME without spaces (eg: Airborne_HIV) or hit OK to leave blank: "
            set dialogResult to display dialog prompt default answer ""
        end tell

eof-1

}
################################################################################
# function GetLabel lets user customize the labels for F, Sigma, etc. in the 
# output mtz file.

function GetLabel {
    osascript << eof-5
        tell app "Finder"
            activate
            set prompt to "Enter a subscript name for your dataset flags (eg: foo  for F_foo): "
            set dialogResult to display dialog prompt default answer "foo"
        end tell

eof-5

}

################################################################################
# function GetSpaceGroup lets user specify the spacegroup (also available on
# line 3 of the sca file.  This gives some flexibility.

function GetSpaceGroup {
    osascript << eof-6
        tell app "Finder"
            activate
            set prompt to "Enter a Space Group name or Number (eg: P212121): "
            set dialogResult to display dialog prompt default answer "P1"
        end tell

eof-6

}

################################################################################
# function GetNumAA lets user specify an estimated number of amino acids in the
# asymmetric unit of the crystal for quasi-absolute scaling with truncate
# The number isn't critical; I let it default to 150.

function GetNumAA {
    osascript << eof-7
        tell app "Finder"
            activate
            set prompt to "Estimate the sum of the number of amino acids and 3 times the number of nucleotides in the ASU (eg: 150): "
            set dialogResult to display dialog prompt default answer "150"
        end tell

eof-7

}

################################################################################

# function ChooseFile allows picking from filtered list of files in $PWD
# returns name of chosen file as a string

function ChooseScaFile {
#
# Change this first line for particular filtering needs:
#
# =========>
#
	filelist=($( command ls -1d *.sca )) 
#
	if [[ -z $filelist ]];then
		return 1
	fi

	item_list="" 

	for item in "${filelist[@]}" 
	do 
		item_list="$item_list""\"${item}\"," 
	done 

	function filepicker {
		osascript << eof 
			tell app "Finder" 
				activate 
				choose from list {${item_list%,}} with prompt "Pick one: " 
			end tell
eof
	} 

	SelectedFile=$(filepicker) 

	print "$SelectedFile"

}
################################################################################

# Function for buttons
# User must supply $buttonDialog

function buttonfuncKey { 
osascript <<-eof
	tell app "Finder"
	activate
	set r to display dialog "$buttonDialog" \
       buttons {"Display", "Dismiss"} default button "Display" giving up after 10
    set favoriteApp to button returned of r
    end
eof
}


function buttonfuncKey2 { 
osascript <<-eof
	tell app "Finder"
	activate
	set r to display dialog "$buttonDialog2" \
       buttons {"YES", "NO"} default button "YES" giving up after 10
    set favoriteApp to button returned of r
    end
eof
}

#################################################################################

# Now for the actual programs:

# If the sca file is not provided as an argument, querry user for the filename.

if [[ $# == 1 ]]; then

   scalepack_file=$1

elif [[ $# == 0 ]];then

   scalepack_file=$(ChooseScaFile)

else 

  scalepack_file=$1
  print "Reducing $scalepack_file only.  Ignoring other input."
  print ""
fi

#############################################################################

# Get the Project Name

 
    PROJECTNAME=$(GetProjectName | cut -d: -f3)
 

print "You have chosen $PROJECTNAME as the project name"
 
#############################################################################

# Get the estimated asymmetric unit content.


    nresidue=$(GetNumAA | cut -d: -f3)



print "Estimate asymmetric unit content as $nresidue amino acids."
 


#############################################################################

# Label assignment:

# Assign the labels for the data used in truncate

    fobslabel=$(GetLabel | cut -d: -f3)
 

print "You have chosen the data label subscript $fobslabel"

#############################################################################

# Get the space group

    spacegroup=$(GetSpaceGroup | cut -d: -f3)
 

print "You have chosen the data label subscript $spacegroup"
 
#############################################################################

# get the filename prefix and use it for the output files and title.

mtz_prefix=$scalepack_file:r  

if [[ sca == $scalepack_file:e ]]; then

	print "You chose file $scalepack_file"
    print "Using prefix $mtz_prefix"
	print "Running CCP4 scalepack2mtz to convert the data .................."

else
	print "There are either no sca files present in this directory: $PWD"
    print "or you have not chosen any of them because you cancelled the selection."
	print "Program terminating..."
	return 1
fi

################################################################################
################################################################################

# Now run the CCP4 scalepack2mtz program with the user-supplied input:

################################################################################

#
#  h k l I+ SigI+ I- SigI-   were extracted from aucn.na4
#  (acentric data only), and put into scalepack format. 
#  This is simply to illustrate the procedure for getting 
#  scalepack data into CCP4. I don't really know if it
#  is a good example.
#
#  (You can use the same procedure whether or not you have 
#  anomalous data.)

#  Compulsory inputs are SYMMETRY followed by space group no.
#  PROJECTNAME, CRYSTALNAME,DATAsetNAME and Wavelength.

scalepack2mtz hklin $scalepack_file \
              hklout /tmp/junk1.mtz <<eof
PROJECTNAME $PROJECTNAME
CRYSTALNAME $mtz_prefix
DATAsetNAME $mtz_prefix_$fobslabel
SYMMETRY $spacegroup
end
eof

print ""
print "The DATAsetNAME specified is $mtz_prefix_$fobslabel"
print "The CRYSTALNAME specified is $mtz_prefix "
print "The PROJECTNAME specified is $PROJECTNAME "
print ""
sleep 2
print "Truncating the data ............."

#############################################################################
#
# CCP4 Truncate converts intensities to amplitudes:  I(hkl) to F(hkl), DANO(hkl)
#
#############################################################################

truncate hklin /tmp/junk1.mtz \
         hklout /tmp/junk2.mtz \
         <<EOF-trunc >| truncate_run1_log.html                    
title $mtz_prefix dataset
truncate yes
nresidue $nresidue
PNAME $PROJECTNAME
DNAME $mtz_prefix_$fobslabel
labout  F=F_$fobslabel  SIGF=SIGF_$fobslabel DANO=DANO_$fobslabel SIGDANO=SIGDANO_$fobslabel  
EOF-trunc

buttonDialog="Shall I display the Truncate log file in the Camino web browser?"

if [[ $(buttonfuncKey) != Dismiss ]];then
   open -a Camino truncate_run1_log.html
   sleep 5
   buttonDialog=""
fi
 

if [[ ! -e /tmp/junk2.mtz ]]; then
	print "Truncation error.  Program terminating..."
    print "Please check log file and for possible input mtz file corruption."
	return 1
fi


################################################################################

#  cad data:  sort and put data in CCP4 asymmetric unit  (this is critical)

################################################################################

print ""
print "##################################################################"
print ""
print " Running cad to sort the data into CCP4's asymmetric unit ............."
print ""
print "##################################################################"
print ""
sleep 2


cad hklin1 /tmp/junk2.mtz hklout /tmp/junk3.mtz <<eof
labi file 1 ALL
sort H K L
end
eof
#


################################################################################

#  Uniquify data:  sequester 10% of the data for Free-R

################################################################################

# Complete dataset and add free-R column for 10% of data.
print ""
print "##################################################################"
print ""
print "  Uniqueify the data; flagging 10% of data for Free-R ............."
print ""
print "##################################################################"
print ""
uniqueify -p 0.1 /tmp/junk3.mtz \
                 ${mtz_prefix}_unique.mtz >| /dev/null

# Now look at the resulting dataset:

buttonDialog="Shall I examine the new dataset with mtzdmp?"

if [[ $(buttonfuncKey) != Dismiss ]];then

	mtzdmp ${mtz_prefix}_unique.mtz >| check_${mtz_prefix}_mtzdmp.html
	open -a Camino check_${mtz_prefix}_mtzdmp.html
    sleep 5
   buttonDialog=""
fi


# /bin/rm -f /tmp/junk_${mtz_prefix}*.mtz

print ""
print "##################################################################"
print "##################################################################"
print ""
print "    Saving final dataset ${mtz_prefix}_unique.mtz in $PWD "
print ""
print "##################################################################"
print "##################################################################"
print ""

buttonDialog="Shall I display the dataset with HKLVIEW?"

if [[ $(buttonfuncKey) != Dismiss ]];then

	hklview ${mtz_prefix}_unique.mtz >| /dev/null &

	open -a X11  # brings hklview window to the front
    sleep 5
   buttonDialog=""
fi


################################################################################

#  Optional output of dataset in CNS format (a good idea to do it now):

################################################################################


buttonDialog2="Shall I create CNS formatted datasets?"

if [[ $(buttonfuncKey2) != NO ]];then


# Non-anomalous data:
print ""
print "    Formatting data for CNS using mtz2various ......."
print ""
mtz2various HKLIN ${mtz_prefix}_unique.mtz \
            HKLOUT iso_${mtz_prefix}.hkl << EOF-mtz2cns  >| /dev/null
RESOLUTION 100000 0.5
OUTPUT XPLOR
LABIN FP=F_${fobslabel}    SIGFP=SIGF_${fobslabel}   FREE=FreeR_flag
# LABIN FP=DANO_${mtz_prefix}    SIGFP=SIGDANO_${mtz_prefix}  FREE=FreeR_flag        
END
EOF-mtz2cns


buttonDialog2="Shall I create a CNS formatted dataset for Anomalous data?"

if [[ $(buttonfuncKey2) != NO ]];then

# Anomalous data:
mtz2various HKLIN ${mtz_prefix}_unique.mtz \
            HKLOUT dano_${mtz_prefix}.hkl << EOF-mtz2cns >| /dev/null
RESOLUTION 100000 0.5
OUTPUT XPLOR
LABIN FP=F_${fobslabel}    SIGFP=SIGF_${fobslabel}   FREE=FreeR_flag DP=DANO_${fobslabel}    SIGDP=SIGDANO_${fobslabel}     
END
EOF-mtz2cns
fi

# Edit the cns hkl files to change FOBS, SIGMA and TEST to something else


perl -pi -e "s|FOBS|F${fobslabel}|g"      iso_${mtz_prefix}.hkl
perl -pi -e "s|SIGMA|SIG${fobslabel}|g"   iso_${mtz_prefix}.hkl
perl -pi -e "s|TEST|TEST${fobslabel}|g"   iso_${mtz_prefix}.hkl

perl -pi -e "s|FOBS|F${fobslabel}|g"     dano_${mtz_prefix}.hkl
perl -pi -e "s|SIGMA|SIG${fobslabel}|g"  dano_${mtz_prefix}.hkl
perl -pi -e "s|TEST|TEST${fobslabel}|g"  dano_${mtz_prefix}.hkl



print ""
print "##################################################################"
print "##################################################################"
print ""
print "    Saving final CNS datasets as iso_${mtz_prefix}.hkl"
print "    and (if applicable) dano_${mtz_prefix}.hkl in $PWD "
print ""
print "##################################################################"
print "##################################################################"
print ""



fi

buttonDialog=""
buttonDialog2=""
################################################################################

rm -i /tmp/junk*.mtz

 



